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geo2r now returns a CAPTCHA page to scripted requests, which broke CI on master. The test stubs the metadata call, and _create_metadata raises a clear error when the response is not JSON.
This was referenced Sep 23, 2026
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What
test_series_has_no_matrix_data_errorfails on every PR right now, including #216. NCBI's geo2r backend (/geo/geo2r/backend/?type=samples...) now returns a Google reCAPTCHA page with status 200 to scripted requests, soresponse.json()raisesJSONDecodeErrorbefore the test gets to the matrix check it is actually about.How
AutoScanGeoMatrixParser._create_metadata, so it still downloads the real GSE121633 matrix and assertsNoMatrixDataError, without depending on geo2r._create_metadatacallsraise_for_status()and turns a non-JSON body into aValueErrorthat names the URL and says NCBI may be blocking automated requests. Before, users got a bareExpecting value: line 1 column 1.test_metadata_query_non_json_response_errorcovers that error.Heads up
This fixes CI, not the loader. Real
AutoScanGeoMatrixParserloads of the ~2,165 entries ingeo_autoscan_library.yamlwill fail while geo2r keeps serving the CAPTCHA; they now fail with a readable message. A proper fix would read metadata from the series matrix header instead of geo2r, and belongs in its own PR.Tests
make check-formatclean.make test: 202 passed, 5 skipped, 0 failed.